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655 results for “constrain”
Genomic structural variants constrain and facilitate adaptation in natural populations of Theobroma cacao, the Chocolate Tree
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Data from: Functional coupling constrains craniofacial diversification in Lake Tanganyika cichlids
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Data from: The power of evolutionary rescue is constrained by genetic load
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Hybridization constrains the evolution of mimicry complexes in woodpeckers
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Data from: Noradrenergic projections from the locus coeruleus to the amygdala constrain fear memory reconsolidation
<p>Memory reconsolidation is a fundamental plasticity process in the brain that allows established memories to be changed or erased. However, certain boundary conditions limit the parameters under which memories can be made plastic. Strong memories do not destabilize, for instance, although why they are resilient is mostly unknown. Here, we extend the understanding of the mechanisms implicated in reconsolidation-resistant memories by<i> </i>investigating the hypothesis that specific modulatory signals shape memory formation into a state that lacks lability. We find that the activation of the noradrenaline-locus coeruleus system (NOR-LC) during strong fear memory encoding increases molecular mechanisms of stability at the expense of lability in the amygdala. Preventing the NOR-LC from modulating strong fear encoding results in the formation of memories that can undergo reconsolidation within the amygdala and thus are vulnerable to post-reactivation interference. Thus, the memory strength boundary condition on reconsolidation is set at the time of encoding by the action of the NOR-LC.</p>
Data products for "Constraining the second half of reionization with the Lyman-β forest"
<p>Data products for the paper "Constraining the second half of reionization with the Lyman-beta forest" (https://arxiv.org/abs/1912.05582)</p>
Repository - Ganymede's far-ultraviolet reflectance: constraining impurities in the surface ice
<p>This repository contains the modeled spectra and material optical properties used to produce Figures 3-11 in the main text, and the supplementary figures.</p>
Figure 1 in Does nutritional status constrain adoption of more costly and less risky foraging behaviour in an Amazonian shelter-building spider?
Figure 1. Hingstepeira folisecens (Hingston 1932) (Araneae: Araneidae) of Central Amazonia, Brazil. (a) Orb web of H. folisecens with the shelter formed by dry curled leaf (scale: 1 cm). (b) A sub-adult female of H. folisecens (scale: 1 mm).
Data from: High content imaging of unbiased chemical perturbations reveals that the phenotypic plasticity of the actin cytoskeleton is constrained
Although F-actin has a large number of binding partners and regulators, the number of phenotypic states available to the actin cytoskeleton is unknown. Here, we quantified 74 features defining F-actin and cellular morphology in >25 million cells after treatment with a library of 114,400 structurally diverse compounds. After reducing the dimensionality of these data, we found that only ~25 recurrent F-actin phenotypes emerged, each defined by distinct quantitative features that could be machine learned. We identified 2003 unknown compounds as inducers of actin-related phenotypes, including two that directly bind talin, a core regulator of integrin activity. Moreover, we observed that compounds with distinct molecular mechanisms could induce equivalent phenotypes and that initially divergent cellular responses could converge over time. These findings suggest a conceptual parallel between the actin cytoskeleton and gene regulatory networks; where the theoretical plasticity of interactions is nearly infinite, yet phenotypes observed in vivo are constrained into a limited subset of practicable configurations.
Data from: Increased soil temperature and decreased precipitation during early plant life stages constrain grass seedling recruitment in cold desert restoration
1. Seed-based restoration is one of the most difficult challenges for dryland restoration. Identifying environmental conditions that drive variation in seed and seedling mortality across similar restoration efforts could increase understanding of when and where restoration outcomes are likely to be favorable and identify new tools and strategies to improve outcomes. 2. We asked how variation in a suite of environmental predictors influenced germination, emergence, seedling establishment, and juvenile survival of four commonly sown perennial grass species across 33 seeding experiments distributed over a ~160,000-km2 area of the Great Basin, a cold desert system in the western United States. 3. Across experiments, we observed wide variation in the rates of four demographic transitions and wide variation in environmental conditions experienced by plants at each stage. For all species, higher precipitation during the first 30 days following seeding was associated with an increase in germination. Conversely, higher soil temperature over this same time period was associated with a significant decrease in germination and emergence and soil temperature was associated with a substantial portion of the variation in germination and emergence probabilities observed across our seeding experiments. 4. Within the range of precipitation variation observed, we were unable to detect a significant relationship between seedling establishment the first growing season and cumulative precipitation the first year, precipitation during the first spring growing season, or annual climatic water deficit (CWD) the first year. Higher CWD the second growing season reduced seedling survival over that time period. 5. Synthesis and application. Our results show higher soil temperature negatively impacts grass seedling recruitment. Our results can be combined with seasonal and subseasonal temperature forecasts to improve restoration decision-making. These results also suggest climate warming will make restoration even more difficult, with our model estimates suggesting the 2°C increase in temperature expected in the Great Basin over the coming decades will decease germination and emergence by about 30%. Lastly, while our field-based approach provided insight into short-term drivers of mortality, it did not provide insight into drivers of longer-term survival, suggesting a need to develop process-based approaches for predicting long-term restoration outcomes.29-Aug-2019
Datasets for Constraining the Parameter Regime of Pulsar Radio Emission
<p>The datasets support the figures in the paper <em>Refining pulsar radio emission due to streaming instabilities: Linear theory and PIC simulations </em>(figures <span class="math-tex">\(2\)</span> to <span class="math-tex">\(7\)</span>) and provide additional information discussed in Section <span class="math-tex">\(5\)</span> of the paper. They contain parametric studies investigating a relativistic dispersion relation for an electron-positron pair plasma near a pulsar. The investigated quantities are the maximum growth rates (max_growth_rate) in units of <span class="math-tex">\(10^{-3}\omega_\mathrm{p}\)</span>, an integrated value over the entire range of positive wave growth (int_growth_rate) in units of <span class="math-tex">\(10^{-3}\omega_\mathrm{p}\)</span>, the fractional bandwidth (bandwidth) in units of <span class="math-tex">\(\omega_\mathrm{p}\)</span>, the minimum and maximum values where the growth rate exceeds a threshold value of <span class="math-tex">\(2.8\times10^{-4}/\omega_\mathrm{p}\)</span> - which can be associated to effective wave growth - in units of <span class="math-tex">\(1 / d_\mathrm{e}\)</span> (k_thr_min and k_thr_max) as well as a relative deviation of the range between these two values and the entire range of positive wave growth (rel_dev). All of these parameters are investigated while changing a specific parameter in the dispersion relation (<span class="math-tex">\(\rho_0\)</span>, <span class="math-tex">\(\rho_1\)</span>, simultaneously <span class="math-tex">\(\rho_0\)</span> and <span class="math-tex">\(\rho_1\)</span>, <span class="math-tex">\(\epsilon_\mathrm{n}\)</span> and <span class="math-tex">\(\gamma_\mathrm{b}\)</span>, the latter once with <span class="math-tex">\(\epsilon_\mathrm{n}=10^{-3}\)</span> and once with fixed <span class="math-tex">\(n_0 = n_1 =1\)</span>and variable <span class="math-tex">\(\epsilon_\mathrm{n}=10^{-3}\)</span>). These parameters appear in the titles of the text files which contain the respective dataset.</p>
Transit time constrained Canad instances
<p>Transit time constrained adaptations of the Canad instances by A. Frangioni (2012), used in the paper " On Transit Time Constrained Fixed Charge Multi-commodity Flow Problems". Each instance starts with three numbers (N,A,K), representing the number of nodes, arcs and commodities in the instance, respectively. Then follows A lines describing the arcs and K lines describing the commodities. The lines for arcs contain 6 numbers representing, in order: the start node, the end node, the unit flow cost, the capacity, the fixed charge, and the sail time. The lines for commodities contain 4 lines: the start node, the end node, quantity and the transit time. Transit times are at a base level and should be scaled up depending on how tight time constraints one wants. In the paper, mostly a factor of 1.2 was used.</p> <p> </p> <p>The original instances can be found at: http://groups.di.unipi.it/optimize/Data/MMCF.html [25 sep 2020]</p> <p> </p>
IS-mediated mutations both promote and constrain evolvability during a long-term experiment with bacteria
<p>The long-term dynamics of IS elements and their effects on bacteria are poorly understood, including whether they are primarily genomic parasites or important drivers of adaptation by natural selection. Here, we investigate the dynamics of IS elements and their contribution to genomic evolution and fitness during a long-term experiment with <em>Escherichia coli</em>. This data set includes the Rmd file to analyze the genomic and metagenomic data (Tenaillon et al. 2016 and Good et al. 2017) in light with the IS dynamics and their correlation with fitness improvements described in the present work. </p>
Genetic population structure constrains local adaptation in sticklebacks
<p class="MsoBodyText"><span><span><span><span><span><span><span><span><span><span><span>Repeated and independent adaptation to specific environmental conditions from standing genetic variation is common. However, if genetic variation is limited, the evolution of similar locally adapted traits may be restricted to genetically different and potentially less optimal solutions or prevented from happening altogether. Using a quantitative trait locus (QTL) mapping approach, we identified the genomic regions responsible for the repeated pelvic reduction (PR) in three crosses between nine-spined stickleback populations expressing full and reduced pelvic structures. In one cross, PR mapped to linkage group 7 (LG7) containing the gene<i> Pitx1</i>, known to control pelvic reduction also in the three-spined stickleback. In the two other crosses, PR was polygenic and attributed to ten novel QTL, of which 90% were unique to specific crosses. When screening the genomes from 27 different populations for deletions in the <i>Pitx1</i> regulatory element, these were only found in the population in which PR mapped to LG7, even though the morphological data indicated large effect QTL for PR in several other populations as well. Consistent with the available theory and simulations parameterised on empirical data, we hypothesise that the observed variability in genetic architecture of PR is due to heterogeneity in the spatial distribution of standing genetic variation caused by >2x stronger population structuring among freshwater populations and >10x stronger genetic isolation by distance in the sea in nine-spined sticklebacks as compared to three-spined sticklebacks.</span></span></span></span></span></span></span></span></span></span></span></p>
Data from: Hibernation constrains brain size evolution in mammals
The expensive brain hypothesis predicts that the lowest stable level of steady energy input acts as a strong constraint on a species' brain size, and thus that periodic troughs in net energy intake should select for reduced brain size relative to body mass. Here, we test this prediction for the extreme case of hibernation. Hibernators drastically reduce food intake for up to several months, and are therefore expected to have smaller relative brain sizes than non‐hibernating species. Using a comparative phylogenetic approach on brain size estimates of 1104 mammalian species, and controlling for possible confounding variables, we indeed found that the presence of hibernation in mammals is correlated with decreased relative brain size. This result adds to recent comparative work across mammals and amphibians supporting the idea that environmental seasonality (where in extremis hibernation is necessary for survival) imposes an energetic challenge, and thus acts as an evolutionary constraint on relative brain size.
Data from: Brood size constrains the development of endothermy in blue tits
Altricial birds are unable to maintain body temperature when exposed to low ambient temperatures during the first days after hatching. Thermoregulatory capacity begins to form as postnatal development progresses, and eventually nestlings become homeothermic. Several factors may influence this development at both the level of the individual and the level of the whole brood, but to our knowledge no studies have focused on the effect of brood size per se on the development of endothermy in individual nestlings. We performed cooling experiments on blue tit (Cyanistes caeruleus) nestlings in the field, to study how different experimental brood sizes affected the development of endothermy in individual nestlings and the thermal environment experienced by the whole brood in the nest. Nestlings from all experimental brood sizes showed a decrease in cooling rate as they grew older, but birds from reduced broods showed an earlier onset of endothermy compared with nestlings from enlarged and control broods. This difference manifested during early development and gradually disappeared as nestlings grew older. The thermal environment in the nests differed between treatments during nestling development, such that nest temperature in reduced broods was lower than that in enlarged broods during all days and during nights at the end of the experimental period. We suggest that the development of endothermy in blue tit nestlings is not ontogenetically fixed, but instead may vary according to differences in developmental, nutritional and thermal conditions as determined by brood size.
Data from: Depth and vertical hydrodynamics constrain the size–structure of a lowland streambed community
Abundance-body mass (N–M) relationships are prominent macroecological patterns and provide an integrated measurement of the structure and energy flow through natural communities. However, little is known about how N-M relationships are constrained by local environmental conditions. Here we quantify how sediment depth and direction of surface–groundwater exchange (vertical hydrodynamics), two major drivers of the streambed ecology, determine N-M scaling in a sandy lowland, European stream. Streambed assemblages included flagellates, ciliates, meiofauna and macroinvertebrates, and spanned five orders of magnitude in body mass. We detected a significant interaction of body mass with depth and vertical hydrodynamics with a sharp reduction in N–M slopes in the hyporheic zone and under upwelling conditions. These results revealed that streambed assemblages become more size–structured as environmental constraints increase with direct implications for the metabolic capacity and functioning of the system.
Data from: Generalized movement strategies for constrained consumers: ignoring fitness can be adaptive
Movements made by real organisms---such as movements involved in dispersal, migration, and habitat selection---are expected to be suboptimal occasionally due to realistic constraints imposed by incomplete information, perceptual limitations, and stochasticity. Previous theory considering such constraints has shown that movements appropriately conditioned upon habitat or resource characteristics can balance out suboptimal components of movement and thereby lead organisms to ideal free distributions and fitness maxima, whereas movements conditioned upon fitness differentials cannot. These findings suggest a somewhat paradoxical hypothesis: even if organisms have information about their fitness, movement strategies that maximize fitness may be conditioned upon something other than fitness per se. We test this hypothesis by investigating the evolutionary stability of generalized, conditional movement strategies that vary in their use of information on fitness versus information on habitat characteristics. We show that when costs of sensory machinery are included, natural selection should favor movement strategies that completely ignore fitness information. Finally, we synthesize previous work by showing how several previous important theoretical results on adaptive movement strategies are united under our one general model.
Data from: Response to selection on cold tolerance is constrained by inbreeding
The evolutionary potential of any given population is of fundamental importance for its longer-term prospects. Modern land-use practices often result in small and isolated populations, increasing extinction risk through reduced genetic diversity caused by inbreeding or drift. Concomitant genetic erosion may further interfere with a population's evolutionary potential. In this study we investigate the consequences of inbreeding on evolutionary potential (the ability to increase cold resistance) in the tropical butterfly Bicyclus anynana. We applied artificial selection to chill-coma recovery time, starting from three levels of inbreeding (outbred control, one or two full-sib matings). Ten generations of selection produced highly divergent phenotypes, with the lines selected for increased cold tolerance showing by ca. 28% shorter recovery times after cold exposure relative to unselected controls. Correlated responses to selection in 10 life history and stress resistance traits were essentially absent. Inbred lines showed a weaker response to selection, thus indicating a reduced evolutionary potential. Inbreeding depression was still measurable in some traits after the course of selection. Traits more closely related to fitness showed a clear fitness rebound, suggesting a trait-specific impact of purging. Our findings have important implications for the longer-term survival of small populations in fragmented landscapes.
Data from: Y-chromosomes can constrain adaptive evolution via epistatic interactions with other chromosomes
Background: Variation in the non-coding regions of Y-chromosomes have been shown to influence gene regulation throughout the genome in some systems; a phenomenon termed Y-linked regulatory variation (YRV). This type of sex-specific genetic variance could have important implications for the evolution of male and female traits. If YRV contributes to the additive genetic variation of an autosomally coded trait shared between the sexes (e.g. body size), then selection could facilitate sexually dimorphic evolution via the Y-chromosome. In contrast, if YRV is entirely non-additive (i.e. interacts epistatically with other chromosomes), then Y-chromosomes could constrain trait evolution in both sexes whenever they are selected for the same trait value. The ability for this phenomenon to influence such fundamental evolutionary dynamics remains unexplored. Results: Here we address the evolutionary contribution of Y-linked variance by selecting for improved male geotaxis in populations possessing multiple Y-chromosomes (i.e. possessed Y-linked additive and/or epistatic variation) or a single Y-chromosome variant (i.e. possessed no Y-linked variation). We found that males from populations possessing Y-linked variation did not significantly respond to selection; however, males from populations with no Y-linked variation did respond. These patterns suggest the presence of a large quantity of Y-linked epistatic variance in the multi-Y population that dramatically slowed its response. Conclusions: Our results imply that YRV is unlikely to facilitate the evolution of sexually dimorphic traits (at least for the trait examined here), but can interfere with the rate of trait evolution in both males and females. This result could have real biological implications as it suggests that YRV can affect how quickly a population responds to new selective pressures (e.g. invasive species, novel pathogens, or climate change). Considering that YRV influences hundreds of genes and is likely typical of other independently-evolved hemizygous chromosomes, YRV-like phenomena may represent common and significant costs to hemizygous sex determination.
ScienceDex guides
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.